Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome uri icon

abstract

  • A set of 111,090 barley expressed sequencetags (ESTs) was searched for the presence of microsatellitemotifs (simple sequence repeat (SSRs)) andyielded 2,823 non-redundant SSR-containing ESTs(SSR?ESTs). From this, a set of 754 primer pairs wasdesigned of which 525 primer pairs yielded an ampliconand as a result, 185 EST-derived microsatellite loci(EST?SSRs) were placed onto a genetic map of barley.The markers show a uniform distribution along all sevenlinkage groups ranging from 21 (7H) to 35 (3H)markers. Polymorphism information content valuesranged from of 0.24 to 0.78 (average 0.48). To furtherinvestigate the physical distribution of the EST?SSRsin the barley genome, a bacterial artificial chromosomes(BAC) library was screened. Out of 129 markerstested, BAC addresses were obtained for 127 EST?SSR markers. Twenty-seven BACs, forming eightcontigs, were hit by two or three EST?SSRs each. Thisunexpectedly high incidence of EST?SSRs physicallylinked at the sub-megabase level provides additionalevidence of an uneven distribution of genes and thesegmentation of the barley genome in gene-rich andgene-poor regions

publication date

  • 2006
  • 2006